Machine-learning guided discovery of emergent antimicrobial activity from dynamic covalent assemblies（Streptococcus mutans， Pro-DIA(Astrial)）

This dataset contains DIA proteomics data of Streptococcus mutans acquired using a Thermo Scientific Vanquish Neo UHPLC coupled to an Orbitrap Astral mass spectrometer, and includes six biological samples in total: three A5B5-treated samples (A5B5-1, A5B5-2, and A5B5-3) and three PBS-treated control samples (Ctl-1, Ctl-2, and Ctl-3). After tryptic digestion, peptides were separated using a trap column (300 µm × 0.5 cm, 5 μm, Thermo Fisher Scientific) and a C18 analytical column (ES906 PepMap Neo UHPLC, 150 µm × 15 cm, 2 μm, Thermo Fisher Scientific). Mobile phase B consisted of 0.1% formic acid in 80% acetonitrile, and separation was performed at 2.5 µL/min with the following gradient: 0–4 min, 4–25% B; 4–5.8 min, 25–35% B; 5.8–6.2 min, 35–99% B; and 6.2–6.9 min, 99% B. For DIA acquisition, the MS1 scan range was 380–980 m/z with a resolution of 240,000, AGC set to 500%, a 2-Th precursor isolation window, and 300 DIA windows; the normalized collision energy was 25%, and MS2 spectra were acquired over 150–2000 m/z with RF lens set to 50% and a maximum injection time of 3 ms. Raw files were processed in DIA-NN (version 1.8.1) using a researcher-provided database, with trypsin specified as the digestion enzyme, up to one missed cleavage allowed, carbamidomethylation of cysteine set as a fixed modification, oxidation (M) and protein N-terminal acetylation set as variable modifications, and peptide- and protein-level false discovery rates controlled at 1% using a target-reverse strategy.